George, you did see that I said these were the previous version of the CC-M, right? This also happens on the TMCC back-EMF driver from Lionel parts, I tried that one as well, same problem. Like I said, I have used the new "universal" ones without issue in the same configuration.
I am curious what is different about the serial data output, I'll have to look at that some day. I figured that would solve the problem, but the RS Commander acted like the serial data wasn't there when I connected that.